Modulation of mlck-l expression and uses thereof

ABSTRACT

In various aspects and embodiments the invention provides methods and reagents for controlling gene expression, and for treating disorders and diseases. Embodiments provide methods and reagents specifically for the regulation of MLCK expression and for the use thereof in treating disorders and diseases. Various embodiments provide methods and reagents for specifically down regulating the expression of MLCK-L more efficiently than that of MLCK-S, and for the use thereof in treating disorders and diseases. Embodiments provide siNA for the same, particularly siRNAs. Various of the embodiments are useful for the treatment of inflammatory disorders and diseases, including, for one example in the regard, Asthma.

REFERENCE TO RELATED APPLICATIONS

This application claims full right of priority and is acontinuation-in-part application of U.S. Provisional Application Ser.No. 60/841,000 filed on 30 Aug. 2006 which is herein incorporated byreference in its entirety.

FIELD OF THE INVENTION

In various aspects and embodiments the invention relates generally tothe field of gene expression and its control, to reagents and methodstherefore, and to the treatment of disorders and diseases thereby.Various embodiments relate to regulation of MLCK and to interferingnucleic acids therefore. Various embodiments relate to down-regulationof MLCK-L expression without concomitant down regulation of MLCK-S, toreagents and methods therefore, and to the treatment of disorders anddiseases thereby.

BACKGROUND

Increased lung vascular permeability is a hallmark of acute respiratorydistress syndrome (ARDS). It has been established that endotheliumregulates passage of plasma proteins and other macromolecules across thevessel wall and performs the vital task of maintaining the integrity ofthe alveolar-capillary barrier. See Mehta and Malik, Physiol. Rev.,January 2006; 86(1):279-367. Endothelial cells regulate the barrierproperties of the microvessel wall by altering their shape, which wasearlier described as “cell rounding” by Majno and Palade (1961). SeeMajno et al., J. Biophys. Biochem. Cytol., December, 1961: 11:571-605.Cell shape change occurs as a result of actinomyosin-based endothelialcell contraction, requiring myosin light chain (MLC) phosphorylation.See Mehta and Malik, Physiol. Rev., January 2006; 86(1):279-367. Thephosphorylation of MLC is catalyzed by activated myosin light chainkinase (MLCK) in the presence of ionized intracellular calcium andcalmodulin.³ Several studies using either constitutively active MLCK orpharmacological inhibitors of MLCK have shown that MLCK-induced MLCphosphorylation plays an essential role in regulating endothelialpermeability in vitro and in vivo.³⁻¹⁰ In addition, studies indicatethat increased MLCK activity and MLC phosphorylation in endothelial cellmonolayers are required for transendothelial polymorphonuclear (“PMN”)migration elicited by chemotactic agents.^(11, 12) Importantly, recentgene expression profiling studies from several acute lung injurypatients have identified SNPs (single-nucleotide polymorphisms) in theMLCK gene (MYLK) that may be associated with ARDS. MLCK is thusindicated to be a potential therapeutic target for treatingARDS.^(13, 14)

Interestingly, primary endothelial cells are known to express the 210kDa long isoform of MLCK referred to as endothelial MLCK-L and thewell-known 130 kDa smooth muscle MLCK isoform (MLCK-S, as usedherein).^(9, 15-17) These isoforms are encoded from a single gene onchromosome 3. Structurally, MLCK-L contains all the domains present inthe smooth muscle isoform, but in addition, has a unique 922-amino acidN-terminal domain containing consensus sites for phosphorylation bymultiple protein kinases, including cAMP-dependent protein kinase A(PKA), PKC, PAK, Src, and Ca²⁺/CaM-dependent protein kinase II.^(1, 3).The N-terminus of MLCK-L has been shown to interact with Src.³Macrophage inhibitory factor¹⁸ and microtubules¹⁹ also bind with highaffinity to the N-terminus of MLCK-L. Thus, regulation of MLCK-L byserine and tyrosine kinases, and its complexation with multiple proteinsindicate that many signaling pathways may exert control on endothelialpermeability by converging to MLCK-L. However, previous studies usingapproaches which target the kinase activity of MLCK without isoformspecificity have not been clear in identifying the individual role ofMLCK-L in regulating endothelial barrier function. In accordance withvarious aspects and embodiments of the invention herein disclosed ansiRNA sequence that specifically “knocks down” MLCK-L in cultured cellswas developed and used in a recently developed strain of mice lackingMLCK-L (MLCK210^(−/−) mice)⁶ to show the importance of MLCK210 in themechanism of increased lung vascular permeability. A thrombin or a PAR-1peptide agonist was used to elicit an endothelial permeability responsebecause PAR-1 receptor agonists are known to increase endothelialpermeability by actinomyosin induced contraction downstream ofG-protein-coupled proteinase-activated receptor-1 (PAR-1) in endothelialmonolayer as well as in vivo models.¹ The results show that, inaccordance with the invention, MLCK-L is a key effector mediating thePAR-1-induced increase in lung vascular permeability in part throughphosphorylation of MLC and MLCK is involved in regulation of calciumentry via a previously undescribed interaction with store operatedchannels.

SUMMARY

In various aspects and embodiments the invention provides new nucleicacid molecules which down regulate expression and/or stability ofMLCK-L. In various aspects and embodiments the invention providescompounds and methods which are useful in molecular investigations ofMLCK and, additionally, in the diagnosis, prevention, and therapy oftissue inflammation and angiogenesis. In embodiments the compounds arestable nucleic acid agents which may be used to knockdown or downregulate MLCK-L. In embodiments the nucleic acid agent is a siRNA. Inembodiments, the nucleic acids are modified to adjust forsingle-nucleotide polymorphisms which may be reflected in the targetedDNA or RNA molecule(s).

Embodiments of the invention provide a double stranded short interferingnucleic acid (siNA) molecule that directs cleavage of a myosin lightchain kinase (MLCK) RNA, wherein: (a) each strand of said siNA moleculeis about 19 to about 25 nucleotides in length; and (b) one strand ofsaid siNA molecule comprises a region having a nucleotide sequencehaving sufficient complementarity to the MLCK RNA for the siNA moleculeto direct cleavage of the MLCK RNA via RNA interference. In embodimentsthe double-stranded siNA is a siRNA. In embodiments the siNA cleavesMLCK-L RNA more efficiently than MLCK-S RNA. In embodiments the siNAcleaves MLCK-L RNA at least twice as efficiently as it cleaves MLCK-SRNA. In embodiments the siNA specifically cleaves MLCK-L RNA andsubstantially does not cleave MLCK-S RNA. In embodiments, the siRNAcomprises a region having the sequence of SEQ ID NO:3. In embodiments,the siNA is a siRNA.

Embodiments of the invention provide a method for modulating MLCKexpression in a cell, comprising introducing into a cell a doublestranded siNA that cleaves MLCK RNA, wherein (a) each strand of saidsiNA molecule is about 19 to about 25 nucleotides in length; and (b) onestrand of said siNA molecule comprises a region having a nucleotidesequence having sufficient complementarity to the MLCK RNA for the siNAmolecule to direct cleavage of the MLCK RNA via RNA interference. Inembodiments the siNA specifically cleaves MLCK-L RNA and substantiallydoes not cleave MLCK-S RNA. In embodiments, the siNA comprises a regionhaving the sequence of SEQ ID NO:3. In embodiments the siNA is a siRNA.

Embodiments of the invention provide a method for modulating tissueinflammation of a patient suffering therefrom, comprising: administeringto a patient suffering from tissue inflammation a nucleic acid in anamount and by a route effective to modulate said tissue inflammation,wherein said nucleic acid comprises a region complementary to an RNAencoded by an MLCK gene and is effective to direct cleavage specificallyof said RNA by RNA interference. In embodiments the nucleic acid is adouble stranded siNA. In embodiment the nucleic acid is a doublestranded siNA that cleaves MLCK RNA. In embodiment each strand of saidsiNA molecule is about 19 to about 25 nucleotides in length; and onestrand of said siNA molecule comprises a region having a nucleotidesequence having sufficient complementarity to the MLCK RNA for the siNAmolecule to direct cleavage of the MLCK RNA via RNA interference. Inembodiments the siNA specifically cleaves MLCK-L RNA and substantiallydoes not cleave MLCK-S RNA. In embodiments, the siNA comprises a regionhaving the sequence of SEQ ID NO:3. In embodiments, the siNA is a siRNA.

Embodiments of the invention provide a method for treating asthma in apatient suffering therefrom, comprising: administering to a patientsuffering from asthma a nucleic acid in an amount and by a routeeffective to treat asthma, wherein said nucleic acid comprises a regioncomplementary to an RNA encoded by an MLCK gene and is effective todirect cleavage specifically of said RNA by RNA interference. Inembodiments the nucleic acid is a siNA. In embodiments the nucleic acidis a siNA that specifically cleaves MLCK-L RNA and substantially doesnot cleave MLCK-S RNA. In embodiments the nucleic acid comprises aregion having the sequence of SEQ ID NO:3. In embodiments the nucleicacid is a siNA. In embodiments the nucleic acid is a siRNA.

In various embodiments the invention provides methods for modulatingexpression of genes in a patient comprising: administering to a patienta nucleic acid complementary to a target 3′UTR mRNA encoded by a geneexpressed in the endothelium in an amount and by a route effective formodulating the activity of said mRNA in said patient. In embodiments inthis regard the nucleic acid is a siNA. In embodiments the nucleic acidspecifically cleaves MLCK RNAs. In embodiments the nucleic acidspecifically cleaves MLCK-L RNA and substantially does not cleave MLCK-SRNA. In embodiments the nucleic acid is a siNA. In embodiments thenucleic acid is a siRNA. In embodiments the nucleic acid comprises aregion complementary to a region of an MLCK RNA. In embodiments theregion has greater complementary to MLCK-L than to MLCK-S RNA. Inembodiments the region is complementary to all or a part of the sequenceof nucleotides 1428 to 1634 of the sequence of human MLCK-L RNA, as setout in SEQ ID NO. 4. In embodiments the nucleic acid directs cleavage byRNA interference of MLCK specifically in non-smooth muscle cells butsubstantially not in smooth muscle cells. In embodiments the nucleicacid comprises a region having the sequence of SEQ ID NO:1, SEQ ID NO:2,or SEQ ID NO:3.

In embodiments the nucleic acid is effective to treat. Sepsis, AcuteRespiratory Distress Syndrome, Trauma, Inflammation and/or Asthma.

RNA interference refers to the process of sequence-specificpost-transcriptional gene silencing in animals mediated by shortinterfering RNAs (siRNAs) (Zamore et al., 2000, Cell, 101, 25-33; Fireet al., 1998, Nature, 391, 806; Hamilton et al., 1999, Science, 286,950-951; Lin et al., 1999, Nature, 402, 128-129; Sharp, 1999, Genes &Dev., 13:139-141; and Strauss, 1999, Science, 286, 886). Thecorresponding process in plants (Heifetz et al., International PCTPublication No. WO 99/61631) is commonly referred to aspost-transcriptional gene silencing or RNA silencing and is alsoreferred to as quelling in fungi. The process of post-transcriptionalgene silencing is thought to be an evolutionarily-conserved cellulardefense mechanism used to prevent the expression of foreign genes and iscommonly shared by diverse flora and phyla (Fire et al., 1999, TrendsGenet., 15, 358). Such protection from foreign gene expression may haveevolved in response to the production of double-stranded RNAs (dsRNAs)derived from viral infection or from the random integration oftransposon elements into a host genome via a cellular response thatspecifically destroys homologous single-stranded RNA or viral genomicRNA. The presence of dsRNA in cells triggers the RNAi response through amechanism that has yet to be fully characterized. This mechanism appearsto be different from other known mechanisms involving double strandedRNA-specific ribonucleases, such as the interferon response that resultsfrom dsRNA-mediated activation of protein kinase PKR and2′,5′-oligoadenylate synthetase resulting in non-specific cleavage ofmRNA by ribonuclease L (see for example U.S. Pat. Nos. 6,107,094;5,898,031; Clemens et al., 1997, J. Interferon & Cytokine Res., 17,503-524; Adah et al., 2001, Curr. Med. Chem., 8, 1189).

In particular, the instant invention features small nucleic acidmolecules, such as short interfering nucleic acid (siNA), shortinterfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA),and short hairpin RNA (shRNA) molecules and methods used to modulate theexpression of MLCK genes.

A siNA of the invention can be unmodified or chemically-modified. A siNAof the instant invention can be chemically synthesized, expressed from avector or enzymatically synthesized. The instant invention also featuresvarious chemically-modified synthetic short interfering nucleic acid(siNA) molecules capable of modulating MLCK gene expression or activityin cells by RNA interference (RNAi). The use of chemically-modified siNAimproves various properties of native siNA molecules through, forexample, increased resistance to nuclease degradation in vivo and/orthrough improved cellular uptake. Furthermore, siNA having multiplechemical modifications may retain its RNAi activity. The siNA moleculesof the instant invention provide useful reagents and methods for avariety of therapeutic, diagnostic, target validation, genomicdiscovery, genetic engineering, and pharmacogenomic applications.

FIGURES

FIG. 1. Knockdown of endogenous expression of MLCK-L with siRNA

(A) After 48 hr, cells transfected with MLCK-L siRNA sequences (1-3) orcontrol cells were lysed and Western blotted using MLCK antibody todetect protein expression. (B) Plot shows mean±SE of percent reductionin MLCK-L expression after knockdown normalized against MLCK-Lexpression in control cells. * indicates decrease in MLCK-L expressionin seq3 siRNA transfected cells (p<0.05).

Sequence 1 corresponds to: NNGGACUGCGCUGUUAUUGAG. (SEQ ID NO: 1)Sequence 2 corresponds to: NNGUGGAAAGGCUUGCCGUGA. (SEQ ID NO: 2)Sequence 3 corresponds to: NNUGGGCAGCCCAUCCAGUAC. (SEQ ID NO: 3)

FIG. 2. Effect of MLCK-L knockdown on MLC phosphorylation in response tothrombin

(A) Western blot showing MLC phosphorylation in response to thrombin incells transfected with control (cont si) or MLCK-L (Si-MLCK-L) siRNA.Cells were stimulated with thrombin 48 hr post transfection and lysed.Lysates were Western blotted with phosphor-MLC (top panel) or pan MLCAbs (bottom panel) to determine MLC phosphorylation. (B) Scatter plotshowing mean±SEM of MLC phosphorylation normalized to total MLC incontrol or MLCK-L siRNA transfected monolayers (n=3).

FIG. 3. Effect of MLCK-L knockdown on thrombin-induced RhoA signaling

(A) RhoA activity after 2 min thrombin stimulation of control or MLCK-LsiRNA transfected HPAE cells. RhoA activation is measured by theincreased amount of GTP-bound RhoA (top) compared to total amount ofRhoA in whole cell lysates (bottom). (B) MYPT phosphorylation induced bythrombin in control (cont Si) or MLCK-L (Si MLCK) siRNA transfected HPAEcells. Bottom panel shows equal protein loading as anaylyzed by Westernblotting with actin Ab. (C), scatter plot showing mean±SEM of MYPTphosphorylation normalized to actin in control or MLCK-L siRNAtransfected monolayers (n=3).

FIG. 4. Effect of MLCK-L knockdown on store operated calcium entry

Ratiometric measurements of [Ca²⁺]; during extracellular Ca²⁺depletion-repletion conditions after depletion of stores with thrombin(A-B) or thapsigargin (C-D) in cells transfected with control (cont Si;solid line) or MLCK-L siRNA (Si MLCK; broken line). Measurements weremade 48 hr post transfection after loading HPAE cell monolayer with Fura2-AM for 15 min. Each representative tracing is the average response of30-40 cells, and experiments were repeated three times. B and D, plotshows mean±SEM of [Ca²⁺]; following store depletion or Ca²⁺ entry in twogroups (n=5). * indicates reduced Ca²⁺ entry in MLCK-L knockdown cellscompared to cells transfected with control siRNA transfected cells(P<0.05).

FIG. 5. MLCK-L knockdown effect on throbin stimulated adcrens junctiondisassembly

Cells transfected with control (Cont Si) or MLCK-L (Si MLCK-L) siRNAwere stimulated with thrombin 48 hr post transfection and fixed followedby staining with VE-cadherin and Alexa-labeled secondary Ab to determineadherens junction dis-assembly by confocal imaging.

FIG. 6. MLCK-L knockdown effect on thrombin stimulated barrierdysfunction

Transendothelial electrical resistance (TER) measurements in HPAE cellstransfected with control (cont Si) or MLCK-L (Si MLCK-L) siRNA. Datarepresent mean±SE from multiple experiments (n=5).

FIG. 7. Effects of PAR-1 agonist peptide on pulmonary microvessel liquidpermeability (K_(fc)) in lungs isolated from Wt or MLCK-L knockout mice

(A) Immunoblot of lung homogenate with MLCK antibody shows absence ofMLCK-L 210 in MLCK^(−/−) mice lungs but expression of 130 KD smoothmuscle MLCK isoform is not affected. (B) After attaining isogravimetricconditions in the lungs, venous pressure was raised to 10 cm H₂O todetermine changes in K_(f,c). Results are mean±SE of 4 experiments. C,PAR-1 peptide induced vasoconstrictor response in lungs isolated from Wtor MLCK^(−/−) mice.

FIG. 8. Western blot showing unphosphorylated (UP) and phosphorylatedform (P) of mouse lung myosin light chain (MLC)

WT (wild type) or MLCK-L^(−/−) lung preparations were preperfused for 7min with PAR-1 peptide and MLC phosphorylation was determined by Westernblotting with anti-MLCK antibody following urea gel electrophoresis.

FIG. 9. Inhibition of eye inflammation in mouse model lacking the MLCKgene

Numbers of inflammatory cells in subconjunctival areas in paraffin eyesections were counted. The value was normalized to the number ofinflammatory cells per unit area (2500 μm²) underneath the conjunctivalepithelium. For each treatment at least 4 mice were used.

FIG. 10. MLCK-L siRNA prevents LPS-induced lung injury

After 48 hours mice (C56B1/J) injected with scrambled (Sc) or MLCK-LsiRNA were challenged with PBS or 1 mg/ml LPS through nebulizer for 45min. Lungs were harvested after 4 hr of LPS challenge. Inset: Immunoblotof mouse lung injected with MLCK-L siRNA shows decrease in MLCK-Lprotein expression (210 kD). Note: MLCK-L siRNA had minimal effect onshort (130 kD) smooth muscle MLCK isoform. (A) lung wet-dry-weight ratioin mice receiving Sc or MLCK-SiRNA. (B) albumin accumulation in mouselungs receiving Sc or MLCK-SiRNA. Evans-blue tagged albumin was injectedinto vasculature of 30 min before terminating the experiment andaccumulation of Evans-blue was determined. (C-D) Inflammatory cellsaccumulation in brochoalveolar lavage of mice receiving Sc orMLCK-SiRNA. Neutph, neutrophils; Bas, basophils; Eos, eosinophils;lymph, lymphocytes; macroph, macrophages.

DESCRIPTION

The present invention relates to compounds and methods which are usefulin molecular investigations of MLCK, and, in the diagnosis, prevention,and therapy of tissue inflammation and angiogenesis. These compounds arestable nucleic acid agents which may be used to knockdown or downregulate MLCK-L. An example of one such nucleic acid agent is a siRNA asherein described.

GLOSSARY

Unless defined otherwise, all technical and scientific terms used hereinhave the same meanings as commonly understood by one of skill in the artto which the disclosed invention belongs. Although any methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the present invention, the preferred methods,devices, and materials are as described.

As used herein, particularly in the claims, the words “a” and “an” meanthe same as the phrases “one and more than one” and “at least one” andexplicitly are not limited to the singular, or to just one. For example,“a host cell” refers to at least one host cell and includes more thanone host cell.

As used herein, particularly in the claims, the word “the” includes theplural as well as the singular and refers to “one or more than one” and“at least one.” For example, “the siRNA” refers to at least one siRNA,and includes one and more than one siRNA.

The word “specifically” as used herein in, particularly as to the phrase“specifically cleaves MLCK-L RNA,” means that at least 50% of all theRNAs that are cleaved are MLCK-L RNAs.

The term “substantially” as used herein, in particular in the phrase“substantially does not cleave” means cleavage does not occur or isinefficient. For instance, in a method of treatment the phase means thatcleavage, to the extent it occurs at all, does not engender deleteriousand/or adverse effects on a patient.

The term “more efficiently” as used herein means greater than.

The term “siRNA” refers to a small interfering RNA(s), which also hasbeen referred to in the art as short interfering RNA and silencing RNA,among others. siRNAs generally are described as relatively short, often20-25 nucleotide-long, double-stranded RNA molecules that are involvedin RNA interference (RNAi) pathway(s). Generally, siRNAs are, in part,complementary to specific mRNAs and mediate their down regulation(hence, “interfering”). siRNAs thus can be used for down regulating theexpression of specific genes and gene function in cells and organisms.siRNAs also play a role in related pathways. The general structure ofmost naturally occurring siRNAs is well established. Generally, siRNAsare short double-stranded RNAs, usually 21 nucleotides long, with twonucleotides single stranded “overhangs” on the 3 of each strand. Eachstrand has a 5′ phosphate group and a 3′ hydroxyl (—OH) group. In vivo,the structure results from processing by the enzyme “dicer,” whichenzymatically converts relatively long dsRNAs and relatively smallhairpin RNAs into siRNAs.

The term siNA refers to a nucleic acid that acts like a siRNA, asdescribed herein, but may be other than an RNA, such as a DNA, a hybridRNA:DNA or the like. siNAs function like siRNAs to down regulateexpression of gene products. See siRNA.

The term “RNA interference” which also has been called “RNA mediatedinterference” refers to the cellular processes by which RNA (such assiRNAs) down regulate expression of genes; i.e., down regulate orextinguish the expression of gene functions, such as the synthesis of aprotein encoded by a gene. Typically, double-stranded ribonucleic acidinhibits the expression of genes with complementary nucleotidesequences. RNA interference pathways are conserved in most eukaryoticorganisms. It is initiated by the enzyme dicer, which cleaves RNA,particularly double-stranded RNA, into short double-stranded fragments20-25 base pairs long. One strand of the double-stranded RNA (called the“guide strand”) is part of a complex of proteins called the RNA-inducedsilencing complex (RISC). The thus incorporated guide strand serves as arecognition sequence for binding of the RISC to nucleic acids withcomplementary sequences. Binding by RISC to complementary nucleic acidsresults in their being “silenced.” The best studied silencing is thebinding of RISCs to RNAs resulting in post-transcriptional genesilencing. Regardless of mechanism, interfering nucleic acids and RNAinterference result in down regulation of the target gene or genes thatare complementary (in pertinent part) to the guide strand.

A polynucleotide can be delivered to a cell to express an exogenousnucleotide sequence, to inhibit, eliminate, augment, or alter expressionof an endogenous nucleotide sequence, or to affect a specificphysiological characteristic not naturally associated with the cell. Thepolynucleotide can be a sequence whose presence or expression in a cellalters the expression or function of cellular genes or RNA. A deliveredpolynucleotide can stay within the cytoplasm or nucleus apart from theendogenous genetic material. Alternatively, DNA can recombine with(become a part of) the endogenous genetic material. Recombination cancause DNA to be inserted into chromosomal DNA by either homologous ornon-homologous recombination.

A polynucleotide-based gene expression inhibitor comprises anypolynucleotide containing a sequence whose presence or expression in acell causes the degradation of or inhibits the function, transcription,or translation of a gene in a sequence-specific manner.Polynucleotide-based expression inhibitors may be selected from thegroup comprising: siRNA, microRNA, interfering RNA or RNAi, dsRNA,ribozymes, antisense polynucleotides, and DNA expression cassettesencoding siRNA, microRNA, dsRNA, ribozymes or antisense nucleic acids.SiRNA comprises a double stranded structure typically containing 15 to50 base pairs and preferably 19 to 25 base pairs and having a nucleotidesequence identical or nearly identical to an expressed target gene orRNA within the cell. An siRNA may be composed of two annealedpolynucleotides or a single polynucleotide that forms a hairpinstructure. MicroRNAs (miRNAs) are small noncoding polynucleotides, about22 nucleotides long, that direct destruction or translational repressionof their mRNA targets. Antisense polynucleotides comprise a sequencethat is complimentary to a gene or mRNA. Antisense polynucleotidesinclude, but are not limited to: morpholinos, 2′-O-methylpolynucleotides, DNA, RNA and the like. The polynucleotide-basedexpression inhibitor may be polymerized in vitro, recombinant, containchimeric sequences, or derivatives of these groups. Thepolynucleotide-based expression inhibitor may contain ribonucleotides,deoxyribonucleotides, synthetic nucleotides, or any suitable combinationsuch that the target RNA and/or gene is inhibited.

Polynucleotides may contain an expression cassette coded to express awhole or partial protein, or RNA. An expression cassette refers to anatural or recombinantly produced polynucleotide that is capable ofexpressing a sequence. The cassette contains the coding region of thegene of interest along with any other sequences that affect expressionof the sequence of interest. An expression cassette typically includes apromoter (allowing transcription initiation), and a transcribedsequence. Optionally, the expression cassette may include, but is notlimited to, transcriptional enhancers, non-coding sequences, splicingsignals, transcription termination signals, and polyadenylation signals.An RNA expression cassette typically includes a translation initiationcodon (allowing translation initiation), and a sequence encoding one ormore proteins. Optionally, the expression cassette may include, but isnot limited to, translation termination signals, a polyadenosinesequence, internal ribosome entry sites (IRES), and non-codingsequences. The polynucleotide may contain sequences that do not serve aspecific function in the target cell but are used in the generation ofthe polynucleotide. Such sequences include, but are not limited to,sequences required for replication or selection of the polynucleotide ina host organism.

A polynucleotide can be delivered to a cell to study gene function.Delivery of a polynucleotide to a cell can also have potential clinicalapplications. Clinical applications include treatment of muscledisorders or injury, circulatory disorders, endocrine disorders, immunemodulation and vaccination, and metabolic disorders (Baumgartner et al.1998, Blau et al. 1995, Svensson et al. 1996, Baumgartner et al. 1998,Vale et al. 2001, Simovic et al. 2001).

A transfection agent, or transfection reagent, or delivery vehicle is acompound or compounds that bind(s) to or complex(es) witholigonucleotides and polynucleotides, and enhances their entry intocells. Examples of transfection reagents include, but are not limitedto, cationic liposomes and lipids, polyamines, calcium phosphateprecipitates, polycations, histone proteins, polyethylenimine,polylysine, and polyampholyte complexes. For delivery in vivo, complexesmade with sub-neutralizing amounts of cationic transfection agent may bepreferred. Non-viral vectors include protein and polymer complexes(polyplexes), lipids and liposomes (lipoplexes), combinations ofpolymers and lipids (lipopolyplexes), and multilayered and rechargedparticles. Transfection agents may also condense nucleic acids.Transfection agents may also be used to associate functional groups witha polynucleotide. Functional groups include cell targeting moieties,cell receptor ligands, nuclear localization signals, compounds thatenhance release of contents from endosomes or other intracellularvesicles (such as membrane active compounds), and other compounds thatalter the behavior or interactions of the compound or complex to whichthey are attached (interaction modifiers).

The term “naked nucleic acids” indicates that the nucleic acids are notassociated with a transfection reagent or other delivery vehicle that isrequired for the nucleic acid to be delivered to a target cell.

“Inhibit” or “down-regulate” means that the expression of the gene, orlevel of RNAs or equivalent RNAs encoding one or more proteins orisoforms, or activity of one or more proteins, such as the MLCK-L orMLCK-S forms, is reduced below that observed in the absence of thenucleic acid molecules of the invention. In one embodiment, inhibitionor down-regulation with the presently described nucleic acid moleculespreferably is below that level observed in the presence of anenzymatically inactive or attenuated molecule that is able to bind tothe same site on the target RNA, but is unable to cleave that RNA. Inanother embodiment, inhibition or down-regulation with antisenseoligonucleotides is preferably below that level observed in the presenceof, for example, an oligonucleotide with scrambled sequence or withmismatches. In another embodiment, inhibition or down-regulation of MLCKwith the nucleic acid molecule of the instant invention is greater inthe presence of the nucleic acid molecule than in its absence.

By “up-regulate” is meant that the expression of the gene, or level ofRNAs or equivalent RNAs encoding one or more proteins or isoforms, oractivity of one or more proteins, such as MLCK-L or MLCK-S, is greaterthan that observed in the absence of the nucleic acid molecules of theinvention. For example, the expression of a gene, such as the MLCK gene,can be increased in order to treat, prevent, ameliorate, or modulate apathological condition caused or exacerbated by an absence or low levelof gene expression.

By “modulate” is meant that the expression of the gene, or level of RNAsor equivalent RNAs encoding one or more protein subunits, or activity ofone or more proteins or protein isoforms is up-regulated ordown-regulated, such that the expression, level, or activity is greaterthan or less than that observed in the absence of the nucleic acidmolecules of the invention.

By “gene” it is meant a nucleic acid that encodes an RNA, for example,nucleic acid sequences including but not limited to structural genesencoding a polypeptide.

“Complimentarity” refers to the ability of a nucleic acid to formhydrogen bond(s) with another RNA sequence by either traditionalWatson-Crick or other non-traditional types. In reference to the nucleicmolecules of the present invention, the binding free energy for anucleic acid molecule with its target or complementary sequence issufficient to allow the relevant function of the nucleic acid toproceed, e.g., enzymatic nucleic acid cleavage, antisense or triplehelix inhibition. Determination of binding free energies for nucleicacid molecules is well known in the art (see, e.g., Turner et al., 1987,CSH Symp. Quant. Biol. LII pp. 123 133; Frier et al., 1986, Proc. Nat.Acad. Sci. USA 83:9373 9377; Turner et al., 1987, J. Am. Chem. Soc.109:3783 3785). A percent complementarity indicates the percentage ofcontiguous residues in a nucleic acid molecule which can form hydrogenbonds (e.g., Watson-Crick base pairing) with a second nucleic acidsequence (e.g., 5, 6, 7, 8, 9, 10 out of 10 being 50%, 60%, 70%, 80%,90%, and 100% complementary). “Perfectly complementary” means that allthe contiguous residues of a nucleic acid sequence will hydrogen bondwith the same number of contiguous residues in a second nucleic acidsequence.

By “RNA” is meant a molecule comprising at least one ribonucleotideresidue. By “ribonucleotide” or “2′-OH” is meant a nucleotide with ahydroxyl group at the 2′ position of a □-D-ribo-furanose moiety.

Nucleic Acid Modification.

Chemically synthesizing nucleic acid molecules with modifications (base,sugar and/or phosphate) that prevent their degradation by serumribonucleases can increase their potency (see e.g., Eckstein et al.,International Publication No. WO 92/07065; Perrault et al., 1990 Nature344, 565; Pieken et al., 1991, Science 253, 314; Usman and Cedergren,1992, Trends in Biochem. Sci. 17, 334; Usman et al., InternationalPublication No. WO 93/15187; and Rossi et al., International PublicationNo. WO 91/03162; Sproat, U.S. Pat. No. 5,334,711; and Burgin et al.,supra; all of these describe various chemical modifications that can bemade to the base, phosphate and/or sugar moieties of the nucleic acidmolecules herein). Modifications which enhance their efficacy in cells,and removal of bases from nucleic acid molecules to shortenoligonucleotide synthesis times and reduce chemical requirements aredesired. (All these publications are hereby incorporated by referenceherein).

There are several examples in the art describing sugar, base andphosphate modifications that can be introduced into nucleic acidmolecules with significant enhancement in their nuclease stability andefficacy. For example, oligonucleotides are modified to enhancestability and/or enhance biological activity by modification withnuclease resistant groups, for example, 2′-amino, 2′-C-allyl, 2′-fluoro,2′-O-methyl, 2′-H, nucleotide base modifications (for a review see Usmanand Cedergren, 1992, TIBS. 17, 34; Usman et al., 1994, Nucleic AcidsSymp. Ser. 31, 163; Burgin et al., 1996, Biochemistry, 35, 14090). Sugarmodification of nucleic acid molecules have been extensively describedin the art (see Eckstein et al., International Publication PCT No. WO92/07065; Perrault et al. Nature, 1990, 344, 565 568; Pieken et al.Science, 1991, 253, 314 317; Usman and Cedergren, Trends in Biochem.Sci., 1992, 17, 334 339; Usman et al. International Publication PCT No.WO 93/15187; Sproat, U.S. Pat. No. 5,334,711 and Beigelman et al., 1995,J. Biol. Chem., 270, 25702; Beigelman et al., International PCTpublication No. WO 97/26270; Beigelman et al., U.S. Pat. No. 5,716,824;Usman et al., U.S. Pat. No. 5,627,053; Woolf et al., International PCTPublication No. WO 98/13526; Thompson et al., U.S. Ser. No. 60/082,404which was filed on Apr. 20, 1998; Karpeisky et al., 1998, TetrahedronLett., 39, 1131; Earnshaw and Gait, 1998, Biopolymers (Nucleic acidSciences), 48, 39 55; Verma and Eckstein, 1998, Annu. Rev. Biochem., 67,99 134; and Burlina et al., 1997, Bioorg. Med. Chem., 5, 1999 2010; allof the references are hereby incorporated in their totality by referenceherein). Such publications describe general methods and strategies todetermine the location of incorporation of sugar, base and/or phosphatemodifications and the like into ribozymes without inhibiting catalysis,and are incorporated by reference herein. In view of such teachings,similar modifications can be used as described herein to modify thenucleic acid molecules of the instant invention.

While chemical modification of oligonucleotide internucleotide linkageswith phosphorothioate, phosphorothioate, and/or 5′-methylphosphonatelinkages improves stability, too many of these modifications can causesome toxicity. Therefore when designing nucleic acid molecules theamount of these internucleotide linkages should be minimized. Thereduction in the concentration of these linkages should lower toxicityresulting in increased efficacy and higher specificity of thesemolecules.

Nucleic acid molecules having chemical modifications that maintain orenhance activity are provided. Such nucleic acid is also generally moreresistant to nucleases than unmodified nucleic acid. Thus, in a celland/or in vivo the activity can not be significantly lowered.Therapeutic nucleic acid molecules delivered exogenously are optimallystable within cells until translation of the target RNA has beeninhibited long enough to reduce the levels of the undesirable protein.This period of time varies between hours to days depending upon thedisease state. Nucleic acid molecules are preferably resistant tonucleases in order to function as effective intracellular therapeuticagents. Improvements in the chemical synthesis of RNA and DNA (Wincottet al., 1995 Nucleic Acids Res. 23, 2677; Caruthers et al., 1992,Methods in Enzymology 211, 3 19 (incorporated by reference herein) haveexpanded the ability to modify nucleic acid molecules by introducingnucleotide modifications to enhance their nuclease stability asdescribed above.

In one embodiment, the invention features a double-stranded shortinterfering nucleic acid (siNA) molecule that down-regulates expressionof a MLCK gene, wherein the siNA molecule comprises about 19 to about 21base pairs, and wherein each strand of the siNA molecule comprises oneor more chemical modifications. In another embodiment, one of thestrands of the double-stranded siNA molecule comprises a nucleotidesequence that is complementary to a nucleotide sequence of a MLCK geneor a portion thereof, and the second strand of the double-stranded siNAmolecule comprises a nucleotide sequence substantially similar to thenucleotide sequence or a portion thereof of the targeted gene. Inanother embodiment, one of the strands of the double-stranded siNAmolecule comprises a nucleotide sequence that is complementary to anucleotide sequence of a MLCK gene or a portion thereof, and the secondstrand of the double-stranded siNA molecule comprises a nucleotidesequence substantially similar to the nucleotide sequence or a portionthereof of the MLCK gene. In another embodiment, each strand of the siNAmolecule comprises about 19 to about 23 nucleotides, and each strandcomprises at least about 19 nucleotides that are complementary to thenucleotides of the other strand. The MLCK gene may comprise, forexample, the sequence referred to in Table I, or a sub-sequence thereof.

In embodiment of the invention the siNA comprises a sequence that hasgreater complementarity to MLCK-L than MLCK-S and directs downregulation of MLCK-L more efficiently than it directs down regulation ofMLCK-S. In embodiments in this regard the siNA contains a region that isat least 90% identical in sequence to a region of MLCK-L in RNA but isless than 50% identical to any region in MLCK-S in RNA. In embodimentsthe siRNA comprises a region having a sequence comprised within theMLCK-L sequence from nucleotides 1428 to 1638 (inclusive) in SEQ/ID NO24 (or its complement). In embodiments said sequence in MLCK-L is notfound in MLCK-S.

TABLE I Homo sapiens myosin light chain polypeptide1 ccatggggga tgtgaagctg gttgcctcgt  kinase isoform 1 (MLCK)cacacatttc caaaacctcc ctcagtgtgg Accession: AY42427061 atccctcaag agttgactcc atgcccctga 5776 by mRNA linearcagaggcccc tgattcatt ttgccccctc Complete CDS;121 ggaacetctg catcaaagaa ggagccaccg alternatively splicedccaagttcga agggcgggtc c ggggttacc 181 cagagcccca ggtgacatgg cacagaaacgggcaacccat caccagcggg ggccgcttcc 241 tgctggattg cggcatccgg gggactttca gccttgtgat tcatgctgtc catgaggagg 301 acaggggaaa gtatacctgt gaagccaccaatggcagtgg tgctcgccag gtgacagtgg 361 agttgacagt agaaggaagt tttgcgaagcagcttggtca gcctgttgtt tccaaaacct 421 taggggatag autteaget tcagcagtggagacccgtcc tagcatctgg ggggagtgcc 481 caccaaagtt tgctaccaag ctgggccgagttgtggtcaa agaaggacag atgggacgat 541 tctcctgcaa gatcactggc cggccecaaccgcaggtcac ctggctcaag ggaaatgttc 601 cactgcagcc gagtgcccgt gtgtctgtgtctgagaagaa cggcatgcag gttctggaaa 661 tccatggagt caaccaagat gacgtgggagtgtacacgtg cctggtggtg aacgggtcgg 721 ggaaggcctc gatgtcagct gaactt cca tccaaggttt ggacagtgcc aataggtcat 781 ttgtgagaga aacaaaagcc accaattcagatgtcaggaa agaggtgacc aatgtaatct 841 caaaggagtc gaagctggac agtctggaggctgcagccaa aagcaagaac tgctccagcc 901 cccagagagg tggctcccca ccctgggctgcaaacagcca gcctcagccc ccaagggagt 961 ccaagctgga gtcatgcaag gactcgcccagaacggcccc gcagaccccg gtccttcaga 1021 agacttccag ctccatcacc ctgcaggccgcaagagttca gccggaacca agagcaccag 1081 gcctgggggt cctatcacct tctggagaagagaggaagag gccagctcct ccccgtccag 1141 ccaccttccc caccaggcag cctggcctggggagccaaga tgttgtgagc aaggctgcta 1201 acaggagaat ccccatggag ggccagagggattcagcatt ccccaaattt gagagcaagc 1261 cccaaagcca ggaggtcaag gaaaatcaaactgtcaagtt cagatgtgaa gtttccggga 1321 ttccaaagcc tgaagtggcc tggttcctggaaggcacccc cgtgaggaga caggaaggca 1381 gcattgaggt ttatgaaaat gctggctcccattacctctg cctgctgaaa gcccggacca 1441 gggacagtgg gacatacagc tgcactgcttccaacgccca aggccaggtg tcctgtagct 1501 ggaccctcca agtggaaagg cttgccgtgatggaggtggc cccctccttc tccagtgtcc 1561 tgaaggactg cgctgttatt gagggccaggattttgtgct gcagtgctcc gtacggggga 1621 ccccagtgcc ceggatcact tggeigetgaatgggcagcc catccagtac gctcgctcca 1681 cctgcgaggc cggcgtggct gagctccacatccaggatgc cctgccggag gaccatggca 1741 cctacacctg cctagctgag aatgccttggggcaggtgtc ctgcagcgcc tgggtcaccg 1801 tccatgaaaa gaagagtagc aggaagagtgagtaccttct gcctgtggct cccagcaagc 1861 ccactgcacc catcttcctg cagggcctctctgatctcaa agtcatggat ggaagccagg 1921 tcactatgac tgtccaagtg tcagggaatccaccccctga agtcatctgg ctgcacaatg 1981 ggaatgagat ccaagagtca gaggacttccactttgaaca gagaggaact cagcacagcc 2041 tttgtatcca ggaagtgttc ccggaggacacgggcacgta cacctgcgag gcctggaaca 2101 gcgctggaga ggtccgcacc caggccgtgctcacggtaca agagcctcac gatggcaccc 2161 agccctggtt catcagtaag cctcgctcagtgacagcctc cctgggccag agtgtcctca 2221 tctcctgcgc catagctggt gacccctttcctaccgtgca ctggctcaga gatggcaaag 2281 ccctctgcaa agacactggc cacttcgaggtgcttcagaa tgaggacgtg ttcaccctgg 2341 ttctaaagaa ggtgcagccc tggcatgccggccagtatga gatcctgctc aagaaccggg 2401 ttggcgaatg cagttgccag gtgtcactgatgctacagaa cagctctgcc agagcccttc 2461 cacgggggag ggagcctgcc agctgcgaggacctctgtgg tggaggagtt ggtgctgatg 2521 gtggtggtag tgaccgctat gggtccctgaggcctggctg gccagcaaga gggcagggtt 2581 ggctagagga ggaagacggc gaggacgtgcgaggggtgct gaagaggcgc gtggagacga 2641 ggcagcacac tgaggaggcg atccgccagcaggaggtgga geagetggac ttccgagacc 2701 tcctggggaa gaaggtgagt acaaagaccctatcggaaga cgacctgaag gagatcccag 2761 ccgagcagat ggatttccgt gccaacctgcaacggcaagt gaagccaaag actgtgtctg 2821 aggaagagag gaaggtgcac agcccccagcaggtcgattt tcgctctgtc ctggccaaga 2881 aggggacttc caagaccccc gtgcctgagaaggtgccacc gccaaaacct gccaccccgg 2941 attttcgctc agtgctgggt ggcaagaagaaattaccagc agagaatggc agcagcagtg 3001 ccgagaccct gaatgccaag gcagtggagagttccaagcc cctgagcaat gcacagcctt 3061 cagggccctt gaaacccgtg ggcaacgccaagcctgctga gaccctgaag ccaatgggca 3121 acgccaagcc tgccgagacc ctgaagcccatgggcaatgc caagcctgat gagaacctga 3181 aatccgctag caaagaagaa ctcaagaaagacgttaagaa tgatgtgaac tgcaagagag 3241 gccatgcagg gaccacagat aatgaaaagagatcagagag ccaggggaca gccccagcct 3301 tcaagcagaa gctgcaagat gttcatgtggcagagggcaa gaagctgctg ctccagtgcc 3361 aggtgtcttc tgacccccca gccaccatcatctggacgct gaacggaaag accctcaaga 3421 ccaccaagtt catcatcctc tcccaggaaggetcactetg ctccgtctcc atcgagaagg 3481 cactgcctga ggacagaggc ttatacaagtgtgtagccaa gaatgacgct ggccaggcgg 3541 agtgctcctg ccaagtcact gtggatgatgctccagccag tgagaacacc aaggccccag 3601 agatgaaatc ccggaggccc aagagctctcttcctcccgt gctaggaact gagagtgatg 3661 cgactgtgaa aaagaaacct gcccccaagacacctccgaa ggcagcaatg ccccctcaga 3721 tcatccagtt ccctgaggac cagaaggtacgcgcaggaga gtcagtggag ctgtttggca 3781 aagtgacagg cactcagccc atcacctgtacctggatgaa gttccgaaag cagatccagg 3841 aaagcgagca catgaaggtg gagaacagcgagaatggcag caagctcacc atcctggccg 3901 cgcgccagga gcactgcggc tgctacacactgctggtgga gaacaagctg, ggcagcaggc 3961 aggcccaggt caacctcact gtcgtggataagccagaccc cccagctggc acaccttgtg 4021 cctctgacat tcggagctcc teactgaccctgtcctggta tggctcctca tatgatgggg 4081 gcagtgctgt acagtcctac agcatcgagatctgggactc agccaacaag acgtggaagg 4141 aactagccac atgccgcagc acctctttcaacgtccagga cctgctgcct gaccacgaat 4201 ataagttccg tgtacgtgca atcaacgtgtatggaaccag tgagccaagc caggagtctg 4261 aactcacaac ggtaggagag aaacctgaagagccgaagga tgaagtggag gtgtcagatg 4321 atgatgagaa ggagcccgag gttgattaccggacagtgac aatcaatact gaacaaaaag 4381 tatctgactt ctacgacatt gaggagagattaggatctgg gaaatttgga caggtctttc 4441 gacttgtaga aaagaaaact cgaaaagtctgggcagggaa gttcttcaag gcatattcag 4501 caaaagagaa agagaatatc cggcaggagattagcatcat gaactgcctc caccccccta 4561 agctggtcca gtgtgtggat gcctttgaagaaaaggccaa catcgtcatg gtcctggaga 4621 tcgtgtcagg aggggagctg tttgagcgcatcattgacga ggactttgag ctgacggagc 4681 gtgagtgcat caagtacatg cggcagatctcggagggagt ggagtacatc cacaagcagg (SEQ ID NO: 4)

Use of the nucleic acid-based molecules of the invention can lead tobetter treatment of the disease progression by affording the possibilityof combination therapies (e.g., multiple antisense or enzymatic nucleicacid molecules targeted to different genes, nucleic acid moleculescoupled with known small molecule inhibitors, or intermittent treatmentwith combinations of molecules (including different motifs) and/or otherchemical or biological molecules). The treatment of subjects withnucleic acid molecules can also include combinations of different typesof nucleic acid molecules.

Therapeutic nucleic acid molecules (e.g., enzymatic nucleic acidmolecules and antisense nucleic acid molecules) delivered exogenouslyare optimally stable within cells until translation of the target RNAhas been inhibited long enough to reduce the levels of the undesirableprotein. This period of time varies between hours to days depending uponthe disease state. These nucleic acid molecules should be resistant tonucleases in order to function as effective intracellular therapeuticagents. Improvements in the chemical synthesis of nucleic acid moleculesdescribed in the instant invention and in the art have expanded theability to modify nucleic acid molecules by introducing nucleotidemodifications to enhance their nuclease stability as described above.

In one embodiment, nucleic acid catalysts having chemical modificationsthat maintain or enhance enzymatic activity are provided. Such nucleicacids are also generally more resistant to nucleases than unmodifiednucleic acid. Thus, in a cell and/or in vivo the activity of the nucleicacid cannot be significantly lowered. As exemplified herein suchenzymatic nucleic acids are useful in a cell and/or in vivo even ifactivity over all is reduced about 10 fold (Burgin et al., 1996,Biochemistry, 35, 14090). Such enzymatic nucleic acids herein are saidto “maintain” the enzymatic activity of an all RNA ribozyme or all DNADNAzyme.

In another aspect of the invention, vectors, preferably expressionvectors, contain nucleic acids encoding one or more siNAs, for example,miRNAs. As used herein, the term “vector” refers to a nucleic acidmolecule capable of transporting another nucleic acid to which it hasbeen linked. One type of a vector is a “plasmid,” which refers to acircular double stranded DNA loop into which additional DNA segments canbe ligated. Another type of vector is a viral vector, wherein additionalDNA segments can be ligated into the viral genome. Certain vectors arecapable of autonomous replication in a host cell into which they areintroduced (e.g., bacterial vectors having a bacterial origin ofreplication and episomal mammalian vectors. Other vectors (e.g.,non-episomal mammalian vectors) are integrated into the genome of a hostcell upon introduction into the host cell, and thereby are replicatedalong with the host genome. Moreover, certain vectors are capable ofdirecting the expression of genes to which they are operatively linked.Such vectors are referred to herein as “expression vectors.” In general,expression vectors of utility in recombinant DNA techniques are often inthe form of plasmids. In the present specification, “plasmid” and“vector” can be used interchangeably as the plasmid is the most commonlyused from of vector. However, the invention is intended to include suchother forms of expression vectors, such as viral vectors (e.g.,replication defective retroviruses, adenoviruses and adeno-associatedviruses), which serve equivalent functions.

The recombinant expression vectors of the invention comprise a nucleicacid of the invention in a form suitable for expression of the nucleicacid in a host cell, which means that the recombinant expression vectorsinclude one or more regulatory sequences, selected on the basis of thehost cells to be used for expression, which is operatively linked to thenucleic acid sequence to be expressed. Within a recombinant expressionvector, “operably linked” is intended to mean that the nucleotidesequence of interest is linked to the regulatory sequence(s) in a mannerwhich allows for expression of the nucleotide sequence (e.g., in an invitro transcription/translation system or in a host cell when the vectoris introduced into the host cell). The term “regulatory sequence” isintended to include promoters, enhancers, and other expression controlelements (e.g., polyadenylation signals). Such regulatory sequences aredescribed, for example, in Goeddel; Gene Expression Technology: Methodsin Enzymology 185, Academic Press, San Diego, Calif. (1990). Regulatorysequences include those which direct constitutive expression of anucleotide sequence in many types of host cell and those which directexpression of the nucleotide sequence only in certain host cells (e.g.,tissue-specific regulatory sequences). It will be appreciated by thoseskilled in the art that the design of the expression vector can dependon such factors as the choice of the host cell to be transformed, thelevel of expression of protein or RNA desired, etc. The expressionvectors of the invention can be introduced into host cells to therebyproduce siNAs, RNAs, proteins or peptides, including fusion proteins orpeptides.

In another embodiment, a nucleic acid of the invention is expressed inmammalian cells using a mammalian expression vector. The recombinantmammalian expression vector may be capable of directing expression ofthe nucleic acid preferentially in a particular cell type (e.g.,tissue-specific regulatory elements are used to express the nucleicacid). Tissue specific regulatory elements are known in the art.Non-limiting examples of suitable tissue-specific promoters include thealbumin promoter, lymphoid-specific promoters, neuron specificpromoters, pancreas specific promoters, and mammary gland specificpromoters. Developmentally-regulated promoters are also encompassed, forexample the murine hox promoters and the □-fetoprotein promoter.

In another aspect the nucleic acid molecules comprise a 5′ and/or a3′-cap structure. By “cap structure” is meant chemical modifications,which have been incorporated at either terminus of the oligonucleotide(see, for example, Wincott et al, WO 97/26270, incorporated by referenceherein). These terminal modifications protect the nucleic acid moleculefrom exonuclease degradation, and can help in delivery and/orlocalization within a cell. The cap can be present at the 5′-terminus(5′-cap) or at the 3′-terminus (3′-cap) or can be present on bothterminis. In non-limiting examples, the 5′-cap includes inverted abasicresidue (moiety), 4′,5′-methylene nucleotide;1-(beta-D-erythrofuranosyl) nucleotide, 4′-thio nucleotide, carbocyclicnucleotide; 1,5-anhydrohexitol nucleotide; L-nucleotides;alpha-nucleotides; modified base nucleotide; phosphorodithioate linkage;threo-pentofuranosyl nucleotide; acyclic 3′,4′-seco nucleotide; acyclic3,4-dihydroxybutyl nucleotide; acyclic 3,5-dihydroxypentyl nucleotide,3′-3′-inverted nucleotide moiety; 3′-3′-inverted abasic moiety;3′-2′-inverted nucleotide moiety; 3′-2′-inverted abasic moiety;1,4-butanediol phosphate; 3′-phosphoramidate; hexylphosphate; aminohexylphosphate; 3′-phosphate; 3′-phosphorothioate; phosphorodithioate; orbridging or non-bridging methylphosphonate moiety (for more details seeWincott et al., International PCT Publication No. WO 97/26270,incorporated by reference herein).

In another embodiment the 3′-cap includes, for example 4′,5′-methylenenucleotide; 1-(beta-D-erythrofuranosyl) nucleotide; 4′-thio nucleotide,carbocyclic nucleotide; 5′-amino-alkyl phosphate; 1,3-diamino-2-propylphosphate, 3-aminopropyl phosphate; 6-aminohexyl phosphate;1,2-aminododecyl phosphate; hydroxypropyl phosphate; 1,5-anhydrohexitolnucleotide; L-nucleotide; alpha-nucleotide; modified base nucleotide;phosphorodithioate; threo-pentofuranosyl nucleotide; acyclic 3′,4′-seconucleotide; 3,4-dihydroxybutyl nucleotide; 3,5-dihydroxypentylnucleotide, 5′-5′-inverted nucleotide moiety; 5′-5′-inverted abasicmoiety; 5′-phosphoramidate; 5′-phosphorothioate; 1,4-butanediolphosphate; 5′-amino; bridging and/or non-bridging 5′-phosphoramidate,phosphorothioate and/or phosphorodithioate, bridging or non-bridgingmethylphosphonate and 5′-mercapto moieties (for more details seeBeaucage and Iyer, 1993, Tetrahedron 49, 1925; incorporated by referenceherein).

The administration of the herein described nucleic acid molecules to apatient can be intravenous, intraarterial, intraperitoneal,intramuscular, subcutaneous, intrapleural, intrathecal, by perfusionthrough a regional catheter, or by direct intralesional injection. Whenadministering these nucleic acid molecules by injection, theadministration may be by continuous infusion, or by single or multipleboluses. The dosage of the administered nucleic acid molecule will varydepending upon such factors as the patient's age, weight, sex, generalmedical condition, and previous medical history. Typically, it isdesirable to provide the recipient with a dosage of the molecule whichis in the range of from about 1 pg/kg to 10 mg/kg (amount of agent/bodyweight of patient), although a lower or higher dosage may also beadministered.

A composition is said to be a “pharmaceutically acceptable carrier” ifits administration can be tolerated by a recipient patient. Sterileposphate-buffered saline is one example of a pharmaceutically acceptablecarrier. Other suitable carriers are well-known in the art. See, forexample, REMINGTON'S PHARMACEUTICAL SCIENCES, I8th Ed. (1990).

For purposes of immunotherapy, an immunoconjugate and a pharmaceuticallyacceptable carrier are administered to a patient in a therapeuticallyeffective amount. A combination of an immunoconjugate and apharmaceutically acceptable carrier is said to be administered in a“therapeutically effective amount” if the amount administered isphysiologically significant. An agent is physiologically significant ifits presence results in a detectable change in the physiology of arecipient patient.

Additional pharmaceutical methods may be employed to control theduration of action of an immunoconjugate in a therapeutic application.Control release preparations can be prepared through the use of polymersto complex or adsorb an immunoconjugate. For example, biocompatiblepolymers include matrices of poly(ethylene-co-vinyl acetate) andmatrices of a polyanhydride copolymer of a stearic acid dimer andsebacic acid. Sherwood et al., Bio/Technology 10:1446-1449 (1992). Therate of release of nucleic acid molecules from such a matrix dependsupon the molecular weight of the molecule, the amount of molecule withinthe matrix, and the size of dispersed particles. Saltzman et al.,Biophysical. J. 55:163-171 (1989); and Sherwood et al., Bio/Technology10:1446-1449 (1992). Other solid dosage forms are described inREMINGTON'S PHARMACEUTICAL SCIENCES, 18th Ed. (1990).

Reducing or Eliminating MLCK-L Expression

The data presented herein establishes the role of the long MLCK isoformin regulating endothelial permeability in the intact microcirculation inresponse to permeability-increasing mediators. This has been shown usinga recently developed strain of mice lacking the long isoform of MLCK(MLCK210^(−/−) mice) and RNA silencing to reduce expression of MLCK-L inhuman endothelial cells. The findings demonstrate that thrombin-inducedincrease in lung microvessel permeability is prevented in MLCK-L^(−/−)mice. In addition, using siRNA which specifically knockdown MLCK-L inhuman endothelial cells, the results show that MLCK-L suppresses theincrease in intracellular Ca²⁺ level induced by thrombin or thapsigarginby impairing SOC activity. The results identify MLCK-L as a key effectormediating the increase in vascular permeability by regulating thephosphorylation of MLC. We uncovered a novel role of MLCK in theapparently direct activation of SOCs leading to an MLCK-mediatedenhancement of calcium entry.

Ultrastructural findings in the lung endothelium and extensive cellculture models have established that cell contraction leading to gapformation between endothelial cells is a primary determinant ofincreased endothelial permeability in response to agonists such asthrombin, histamine, and VEGF.¹ It is known that activation of the PAR-1receptor by thrombin within seconds leads to a rise in intracellularCa²⁺ which is an essential signal inducing activation of theCa²⁺/CaM-dependent MLCK. MLCK causes actinomyosin stress fibers todevelop force.¹ Further, studies showed that thrombin within minutesalso activates the small GTPase RhoA which induces endothelialcontraction. A general and well accepted model of RhoA regulation ofendothelial contraction is that RhoA through its downstream effector,Rho kinase, can increase MLC phosphorylation by phosphorylation-mediatedinhibition of myosin light chain phosphatase activity. Thus,intracellular Ca²⁺ rise, MLCK and RhoA activation, and endothelialcontraction all precede the formation of interendothelial gaps.¹ Studiesusing pharmacologic as well as constitutively active recombinant MLCKprotein established that MLCK by phosphorylating MLC is intimatelyinvolved in regulating endothelial permeability in cultured monolayersor in in vivo models of vascular permeabilityregulation.^(4, 5, 3, 6-10) Likewise, inhibition of both RhoA andRho-kinase has also been shown to prevent the increase in endothelialpermeability.¹ Thus, the question whether RhoA, MLCK, or the calcium ionplays the dominant role in controlling MLC phosphorylation inendothelial cells in response to permeability-increasing mediators isunresolved. In this regard, we showed that suppression of endogenousMLCK-L in human endothelial cells prevented MLC phosphorylation in thepresence of normal RhoA as well as Rho kinase activities. Thus ourresults support the concept that MLCK-L activity is required for MLCphosphorylation to occur and the Rho-ROCK pathway may be able to sustainthis response.

Studies show that Ca²⁺ entry via store-operated cation (SOC) channelsplays a crucial role in sustaining the increase in intracellular Ca²⁺following depletion of endoplasmic reticulum (ER) stores.^(22, 25-30) Wefound that knock-down of MLCK-L significantly inhibited SOC induced Ca²⁺entry either induced by thrombin or thapsigargin. These findings supportprevious studies in which pharmacologic inhibition of MLCK was shown tosuppress SOC-mediated Ca²⁺ entry in endothelial cells.³¹ MLCK-L couldregulate the SOC activation either by phosphorylating the SOC channelsor by maintaining their surface expression.^(1, 32) Findings from ourgroup as well as others have implicated the transient receptor potentialcanonical (TRPC) channels constitute SOC in endothelial cells.¹Additional studies will be required to identify the target of MLCK-L.

Since MLCK-L was required for MLC phosphorylation as well as SOCactivation, we addressed the role of MLCK-L in mediating the increase inendothelial permeability in cultured cells as well as intactmicrocirculation. An important clue that MLCK-L plays an important rolein regulating lung injury was recently provided by Wainwright et al⁶ whodeveloped a strain of mice in which the long isoform of MLCK was deleted(MLCK-L^(−/−)). They demonstrated that in contrast to WT mice i.p.injection of the bacterial product LPS produced significantly lessdamage in the lungs of MLCK-L^(−/−) mice as reflected by interstitialhemorrhage, inflammatory cell infiltrate, and atelectasis.⁶ Furthermore,deletion of MLCK-L in mice enhanced survival during subsequentmechanical ventilation. Because in addition to endothelium, MLCK-L maybe expressed in other non-muscle cells such as neutrophils andmacrophages, it is possible that the protective effect of MLCK-Lobserved in this study could have been due to the altered function ofinflammatory cells. Using an isolated perfused lung model, we showedthat PAR-1 activation did not elicite increased lung microvesselpermeability in MLCK-L^(−/−) mice. In addition, we observed thatPAR-1-induced MLC phosphorylation was decreased in lung tissue takenfrom MLCK-L null mice. We also showed essentially normal PAR-1-inducedpulmonary vasoconstriction in MLCK-L deficient mice indicating that asmooth muscle isoform was functioning in intact lungs as expected. Arecent study similarly found that the MLCK-L deletion did not alter thecontractility response of isolated aortic rings to vasoconstrictor orvasodilator agonists.³³ Thus, the results of the present study identifythe specific role of MLCK-L in the mechanism of endothelial permeabilityincrease in contrast to the short isoform specific to vascular smoothmuscle cells, which mediates vasoconstriction. We also demonstratedusing TER measurement that MLCK-L plays an essential role in regulatingendothelial barrier function because knock-down of MLCK-L inhibited TERresponse in PAR-1.

The data herein show that MLCK-L by inducing an increase in MLCphosphorylation and by augmenting the influx of Ca²⁺ through the SOCchannel is a key regulator of lung endothelial permeability.

Treatment of Endothelial Cells Dysfunctions and Diseases Thereof Such asAsthma, Adult Respiratory Stress Syndrome, Sepsis and Trauma

The vascular endothelium lining the intima of blood vessels dynamicallyregulates a variety of cellular functions including vascular smoothmuscle tone, host-defense reactions, wound healing, angiogenesis, andalso provides a semi-selective barrier for tissue fluid hemostasis. Dysregulation of endothelial function leads to profound leakage of fluidand macromolecules into the lung tissue and airspace, resulting intissue inflammation, a hall mark of Adult Respiratory Distress Syndrome(ARDS), sepsis and trauma. MLCK by monophosphorylating the regulatoryMLC on Ser19 or by di-phosphorylating Ser19/Thr 18 activates cellcontraction which plays an important role in regulating severalendothelial cell functions such as transendothelial PMN migrationelicited by chemotactic agents and cell survival. Several studies usingeither constitutively active MLCK or pharmacological inhibitors of MLCKhave shown that MLCK-induced MLC phosphorylation plays an essential rolein regulating endothelial permeability in vitro and in vivo.Interestingly, endothelial cells and other inflammatory cells have beenshown to predominantly express the long isoform of MLCK-L. Smallnucleotide profiling of ARDS and asthma patients has identified MLCK-Lto be pathogenic. Results using the mouse model, as described above,show that siMLCK-L inhibits enndotoxin-induced loss of lung vascularfunction and, accordingly, indicates effectiveness of MLCK-L siRNA forclinical applications (treatment) of disorders and diseases involvingendothelial cell dysfunction such as, but not limited to ARDS, sepsis,trauma, and asthma.

The invention is further illustrated by way of the followingillustrative examples. However, it is to appreciated that the inventionis not limited to the particular methodologies, protocols, reagents,results or the like described above and/or set forth in the illustrativeexamples. To the contrary, those of skill in the pertinent arts willreadily ascertain from reading the present disclosure a wide variety ofother specific embodiments of the invention that they can realizewithout undue experimentation. A full understanding of the invention andof the claimed subject matter set forth below may be had only by readingthe present disclosure in full in light of the knowledge and insight ofa person skilled in the arts pertinent thereto.

EXAMPLES Example 1 Materials and Protocols for Assessing MicrovesselPermeability in the Mouse Lung

Human-thrombin was obtained from Enzyme Research Laboratories (SouthBend, Ind.). Human pulmonary arterial endothelial (HPAE) cells andendothelial growth medium (EBM-2) were obtained from Clonetics (SanDiego, Calif.). Fura 2-AM, BAPTA-AM and fluorescent antibodies werepurchased from Molecular Probes. Thapsigargin was obtained fromCalbiochem (La Jolla, Calif.). Electrodes for endothelial monolayerelectrical resistance measurements were obtained from Applied Biophysics(Troy, N.Y.). MLCK-L siRNA were custom synthesized by Dharmacon(Lafayette, Colo.). Anti-RhoA, anti-VE-cadherin antibodies andtransfection reagents for siRNA were purchased from Santa CruzBiotechnology (San Diego, Calif.), phospho-Thr850MYPT1 antibody waspurchased from Upstate (Lake Placid, N.Y.) and anti-MLCK Clone K36 waspurchased from Sigma (St Louis, Mich.). Rho activity was determinedusing GST-rhotekin-Rho-binding domain beads from Cytoskeleton (Denver,Colo.). Anti-phosho-MLC antibody was a gift from Dr. Jerold Turner(University of Chicago).

Endothelial Cell Culture

HPAE cells were cultured in T-75 flasks coated with 0.1% gelatin inEBM-2 medium supplemented with 10% FBS. In all experiments, HPAE cellsbetween passage 6 and 8 were used.

Microvessel Permeability Studies in Mouse Lung

We measured microvessel permeability in the wild type and MLCK210^(−/−)mice lung by determining microvascular filtration coefficient (K_(f,c))as described.²⁰ Briefly, according to an approved protocol of theUniversity of Illinois at Chicago Animal Care Committee, male miceweighing 25-30 g were anesthetized with a combination of 10 mg/mlketamine, 0.25 mg/ml xylazine, and 0.25 mg/ml acepromazine and isolatedmouse lungs were prepared and perfused as described.²⁰ All lungpreparations underwent a 20 min equilibration perfusion, and lungs thatwere not isogravimetric at the end of this period were discarded. Aftera 20-min equilibration perfusion, outflow pressure was elevated by 10 cmH₂O for 2 min. The lung wet weight increase over this time, whichreflects the net fluid accumulation, was continuously recorded. At theend of each experiment, lung dry weight was determined. K_(f,c)(ml·min-¹-cmH₂O-g dry wt⁻¹) was calculated from the slope of therecorded weight change normalized to the pressure change and lung dryweight. The expression of MLCL-L in lungs was determined by Westernblotting of lung homogenate with anti-MLCK Ab.

Transfection of siRNA

siRNAs were transfected into cells using Santa Cruz transfection reagentfollowing manufacture's protocol.

Western Blotting

Lysates from HPAE cell monolayers were Western blotted with indicatedantibodies using published protocols.²¹

Cytosolic Ca²⁺ Measurements

An increase in intracellular Ca²⁺ was measured using the Ca²⁺-sensitivefluorescent dye Fura 2-AM as described.^(21, 22)

Measurements of RhoA Activity

RhoA activity was measured using GST-rhotekin-Rho binding domain(GST-RBD) that specifically pulls down activated RhoA asdescribed.^(21, 22)

Immunoflorescence

After stimulation with thrombin, cells were rinsed quickly with ice-coldHBSS, fixed and stained with anti-VE-cadherin Ab followed byalexa-labeled secondary Ab as described previously.²¹

MLC Phosphorylation

Cells stimulated with thrombin were lysed with Laemmli sample buffer andwestern blotted with antibodies for phosphorylated-MLC or pan-MLC Abs todetermine MLC phosphorylation.

Transendothelial Electrical Resistance Measurement

The time course of endothelial cell retraction, a measure of increasedendothelial permeability, was measured using established protocols.²³

Statistical Analysis

Two-tailed Student t-test and one-way ANOVA with Bonferroni post-hoctest were used for statistical comparisons. Differences were consideredsignificant at P<0.05.

Example 2 MLCK-L Knockdown Prevents MLC Phosphorylation without AlteringRhoA Activation

Three siRNA sequences corresponding to the N-terminal region of MLCK-Lwere constructed. Western blot analysis showed that siRNA Seq 3 reducedMLCK-L expression by ˜75% within 48 hr (FIG. 1 A-B). Seq 1, by contrast,was ineffective (FIG. 1A-B). Thus, in the remainder of the study, weused Seq 1 as control for comparison with Seq 3 (i.e. MLCK-L siRNA) toaddress the role of MLCK-L in regulating endothelial barrier function.Thrombin induced MLC phosphorylation in cells transfected with controlsiRNA (FIG. 2). However, “knockdown” of MLCK-L prevented MLCphosphorylation (FIG. 2A-B). A recent study showed that Rho kinase canalso phosphorylate MLC.²⁴ To see if the observed inhibition of MLCphosphorylation is due to altered RhoA-Rho kinase activity in MLCK-Lknock-down cells, we performed a Rho activity assay and also determinedphosphorylation of MYTP-1, a specific Rho kinase substrate. Thrombininduced equivalent RhoA activation in control and in MLCK-L knockdowncells (FIG. 3A). We determined the extent of MYPTI phosphorylation usingan anti-phospho-thr850 MYPT1 antibody. Suppression of MLCK-L had noeffect on thrombin-induced MYPTI phosphorylation (FIG. 3B-C). Thus,these results indicate the essential role of MLCK-L in inducing MLCphosphorylation independently of the Rho/Rho kinase pathway.

Example 3 Impaired Ca²⁺ Influx in MLCK-L Knock-Down Endothelial Cells inResponse to Thrombin or Thapsigargin

We investigated whether calcium entry calcium entry throughstore-operated channels (required for endothelial monolayer retraction)is impaired in MLCK-deficient endothelial cells. We therefore determinedwhether suppression of endogenous MLCK-L affects store-operated calciumentry channels (SOCs) in Fura-2 loaded endothelial monolayer. We usedthrombin to deplete the ER calcium store and elicit calcium entry. Weseparately assessed the calcium-release and calcium-entry componentsusing a Ca²⁺ add-back protocol, which allowed us to determine the roleof MLCK-L in regulating SOC activation. We observed that under Ca²⁺-freebath conditions, MLCK-L knockdown had no effect on thrombin-inducedrelease of Ca²⁺ from stores (FIG. 4A-B). However, suppression of MLCK-Lexpression significantly reduced Ca²⁺ entry upon bath-calcium repletion(FIG. 4A-B).

We used thapsigargin for comparison with thrombin, since thapsigarginactivates SOCs independently of ligand-receptor-G protein-coupledreceptors. Thapsigargin increased Ca²⁺ entry via SOCs (FIG. 4C-D), asexpected. However, suppression of MLCK-L inhibited SOC activation (FIG.4C-D). These findings thereby indicate that MLCK-L regulates SOCchannels independently of G-protein signaling downstream of the PAR-1receptor.

Example 4 MLCK-L Knockdown Prevents Cell Retraction in Response toThrombin

Since our studies show that MLCK-L deficiency led to suppression ofthrombin-induced calcium entry and MLC phosphorylation, we next measuredendothelial cell retraction and paracellular permeability increase inresponse to thrombin. We determined adherens junction organization toassess the effect of MLCK-L knock-down on thrombin-induced junctionaldisassembly, a prerequisite for the increase in endothelialpermeability. We also determined transendothelial electrical resistance(TER) in endothelial monolayers to address the role of MLCK-L inregulating endothelial permeability. As shown in FIG. 5, thrombininduced the disruption of adherens junction in cells transfected withcontrol siRNA. However, this response was not seen in cells transfectedwith MLCK-L siRNA. In endothelial monolayers transfected with controlsiRNA, thrombin caused a decrease in transendothelial monolayerelectrical resistance of ≈55% (FIG. 6). By contrast, exposure ofthrombin to MLCK-L knockdown cells produced only a ≈15% decrease inresistance after thrombin challenge (FIG. 6). Thus, these findingsidentify the specific role of MLCK-L as a key regulator of endothelialbarrier function in response to thrombin.

Example 5 Deletion of MLCK-L in Mice Prevents Increase in Lung VascularPermeability in Response to Selective PAR-1 Receptor Agonist TFLLRNPNDK

We measured microvessel liquid permeability in isolated lungpreparations from wild-type (WT) and MLCK-L^(−/−) mice to determine therole of MLCK-L in regulating lung vascular permeability (FIG. 7A,inset). We found that basal values of K_(f,c) did not significantlydiffer between WT and MLCK-L^(−/−) lungs (FIG. 7A). In wt mice, PAR-1activation produced a 2-3-fold increase in lung K_(f,c) within 15minutes (FIG. 7A). However, this response was not observed in lungs fromMLCK-L^(−/−) mice. We also determined PAR-1-induced pulmonaryvasoconstriction in the MLCK-L^(−/−) mice. Thrombin-inducedvasoconstriction was the same in MLCK-L^(−/−) mouse lung as in the WTmice lung. Thus, these results identify the specific role ofMLCK-L^(−/−) in the mechanism of endothelial permeability increase incontrast to the other isoform specific to vascular smooth muscle cells,which mediates vasoconstriction (FIG. 7B).

We next determined the effect of thrombin on the extent of MLCphosphorylation in mouse lung tissue pretreated with PAR-1 agonist toaddress the possibility that the impairment in lung vascularpermeability is the result of inhibition of MLC phosphorylation. Westernimmunoblots show MLC and phosphorylated MLC (FIG. 8). In lung tissueobtained from normal mice, thrombin induced an increase in MLCphosphorylation. Induction of MLC phosphorylation by thrombin wasdecreased in lung tissue taken from MLCK-L null mice, indicating theessential role of MLC phosphorylation induced by MLCK-L in mediating thethrombin action.

Example 6 Reduction in Eye Inflammation

We observed a significant inhibition of the eye inflammation in themouse lacking the MLCK gene. Wild type or MLCK-L knockout mice wereanesthetized following protocol approved by UIC Animal Care Committee.The subconjunctival scarring was generated by injecting 30 μl of PBScontaining latex beads in the temporal subconjunctival space of themouse's left eye. The beads were 1.053 μm in diameter, 300 μg/ml(Polyscience, Warrington, Pa.). The right eye, which received noinjection, served as an internal control in each group. One-week posttreatment mice were sacrificed by cervical dislocation. Eyes wereremoved by enucleation and fixed in 10% buffered formalin and 5 μm thickparaffin sections were prepared. The sections were stained withhematoxylin and eosin to assess the inflammatory reaction andpicrocirius red to visualize the collagen deposit. The numbers ofinflammatory cells in subconjunctival areas in the sections werecounted. The value was normalized to the number of inflammatory cellsper unit area (2500 μm²) underneath the conjunctival epithelium. Foreach treatment at least 4 mice were used. See FIG. 9.

Example 10 Suppression of Endogenous MLCK-L in Mice Prevents LPS-InducedLung Injury

We used MLCK siRNA to address the possibility that knockdown of MLCK-Lprotects mouse against LPS, a bacterial endotoxin, induced lung injury.As shown in FIG. 1, transduction of MLCK-L siRNA (but not control siRNA)decreased MLCK-L (210) but not smooth muscle isoform (130) expressionafter 48 hr of transfection. We observed that in mice injected withcontrol siRNA, administration of LPS induced a marked increase in lunginflammation as indicated by changes in the lung wet- to dry weightratio, albumin accumulation in the lung and increased number ofinflammatory cells in the bronchioalveolar lavage of mice. However,LPS-induced lung injury was significantly reduced in mice injected withMLCK-L siRNA. See FIG. 10.

REFERENCES

Publications (references) cited herein and the material for which theyare cited are specifically incorporated by reference. Nothing herein isto be construed as an admission that the publication is prior art to theinvention herein disclosed and claimed, or that the publications bearnegatively on patentability of the same, or that the invention is notentitled to antedate any such reference.

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1. A double stranded short interfering nucleic acid (siNA) molecule thatdirects cleavage of a myosin light chain kinase (MLCK) RNA, wherein: (a)each strand of said siNA molecule is about 19 to about 25 nucleotides inlength; and (b) one strand of said siNA molecule comprises a regionhaving a nucleotide sequence having sufficient complementarity to theMLCK RNA for the siNA molecule to direct cleavage of the MLCK RNA viaRNA interference.
 2. A double-stranded siNA, according to claim 1,wherein the siNA is a siRNA.
 3. A double-stranded siNA according toclaim 1, wherein the siNA cleaves MLCK-L RNA more efficiently thanMLCK-S RNA.
 4. A double-stranded siNA, according to claim 3, wherein thesiNA is a siRNA.
 5. A double-stranded siNA according to claim 1, whereinthe siNA cleaves MLCK L RNA at least twice as efficiently as it cleavesMLCK-S RNA.
 6. A double-stranded siNA, according to claim 5, wherein thesiNA is a siRNA.
 7. A double-stranded siRNA, according to claim 1,wherein the siNA specifically cleaves MLCK-L RNA and substantially doesnot cleave MLCK-S RNA.
 8. A double-stranded siNA, according to claim 7,wherein the siNA is a siRNA.
 9. A double-stranded siRNA, according toclaim 7, wherein the siRNA comprises a region having the sequence of SEQID NO:3.
 10. A method for modulating MLCK expression in a cell,comprising introducing into a cell a double stranded siNA that cleavesMLCK RNA, wherein (a) each strand of said siNA molecule is about 19 toabout 25 nucleotides in length; and (b) one strand of said siNA moleculecomprises a region having a nucleotide sequence having sufficientcomplementarity to the MLCK RNA for the siNA molecule to direct cleavageof the MLCK RNA via RNA interference.
 11. A method according to claim10, wherein the siNA specifically cleaves MLCK-L RNA and substantiallydoes not cleave MLCK-S RNA.
 12. A method according to claim 11, whereinthe siNA is a siRNA.
 13. A method according to claim 12, wherein thesiRNA comprises a region having the sequence of SEQ ID NO:3.
 14. Amethod for modulating tissue inflammation in a patient sufferingtherefrom, comprising: administering to a patient suffering from tissueinflammation a nucleic acid in an amount and by a route effective tomodulate said tissue inflammation, wherein said nucleic acid comprises aregion complementary to an RNA encoded by an MLCK gene and is effectiveto direct cleavage specifically of said RNA by RNA interference.
 15. Amethod according to claim 14, wherein said nucleic acid is a doublestranded siNA wherein (a) each strand of said siNA molecule is about 19to about 25 nucleotides in length; and (b) one strand of said siNAmolecule comprises a region having a nucleotide sequence havingsufficient complementarity to the MLCK RNA for the siNA molecule todirect cleavage of the MLCK RNA via RNA interference.
 16. A methodaccording to claim 15, wherein the siNA specifically cleaves MLCK-L RNAand substantially does not cleave MLCK-S RNA.
 17. A method according toclaim 16, wherein the siNA is a siRNA.
 18. A method according to claim17, wherein the siRNA comprises a region having the sequence of SEQ IDNO:3.
 19. A method for treating asthma in a patient suffering therefrom,comprising: administering to a patient suffering from asthma a nucleicacid in an amount and by a route effective to treat asthma, wherein saidnucleic acid comprises a region complementary to an RNA encoded by anMLCK gene and is effective to direct cleavage specifically of said RNAby RNA interference.
 20. A method according to claim 19, wherein thenucleic acid is a siNA. wherein (a) each strand of said siNA molecule isabout 19 to about 25 nucleotides in length; and (b) one strand of saidsiNA molecule comprises a region having a nucleotide sequence havingsufficient complementarity to the MLCK RNA for the siNA molecule todirect cleavage of the MLCK RNA via RNA interference.
 21. A methodaccording to claim 20, wherein the siNA specifically cleaves MLCK-L RNAand substantially does not cleave MLCK-S RNA.
 22. A method according toclaim 21, wherein the siNA is a siRNA.
 23. A method according to claim22, wherein the siRNA comprises a region having the sequence of SEQ IDNO:3.